Abstract: Rural tourism development is an important strategic measure of poverty alleviation. In order to promote the development of rural tourism, Study on the dynamic mechanism and spatial variation is crucial. Taking the southeastern region of Chongqing as an example, we use location theory and spatial organization theory to study the dynamic mechanism of spatial variation. Based on the characteristics of spatial distribution and spatial structure, we restructure the spatial organization of rural tourism destination in southeast Chongqing and establish their spatial relations. The study found that, rural tourism attractions are with a discrete distribution on the whole. Most passenger flows are from major Source to destination, but rarely between tourism attractions. Only a few regions emerge a phenomenon of punctuate polarization, and also axial integration structure is rare in southeastern region of Chongqing. Establishing a growth pole city to attract tourists and share passenger flow is the best way for rural tourism attractions. It means that, we should construct spatial structure system of tourism destination and create a series of passenger flow channels.